[gmx-developers] H-REMD restart

[Luca Bellucci]

hanks Mark for quick replay.
it is 4.5.3
This is the log file at restart point.

-----------------------------------------------------------
Restarting from checkpoint, appending to previous log file.

Log file opened on Sun Jan 23 23:40:07 2011
Host: ionode8  pid: 2916  nodeid: 0  nnodes:  64
The Gromacs distribution was built Thu Nov 18 14:35:49 CET 2010 by
cin0644a at loginfn (Linux 2.6.16.60-0.42.10-ppc64 ppc64)
[..]
Initializing Replica Exchange
Repl  There are 64 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking init_step+nsteps ... OK
Multi-checking first exchange step: init_step/-replex ... OK
Multi-checking the temperature coupling ... OK
Multi-checking the number of temperature coupling groups ... OK
Multi-checking the pressure coupling ... OK
Multi-checking free energy ... OK
[..]
Started mdrun on node 0 Sun Jan 23 23:40:07 2011


> On 24/01/2011 8:57 AM, Luca Bellucci wrote:
> > Dear all,
> > I known that in repl_ex.c is implemented the
> > H-REMD.  It seems to work, however
> > H-REMD is not documented, thus I am testing it.
> > I performed a test  in a BlueGene cluster:
> >
> > mpirun -mode VN -np 4096 mdrun_mpi_bg  -s md.tpr -np 16 -multi 128
> > -replex 2000
> >
> > it works fine.
> >
> > I restarted with this command:
> >
> > mpirun -mode VN -np 4096 mdrun_mpi_bg   -s md.tpr -cpi state.cpt -append
> > -np 16 -multi 128 -replex 2000
> >
> > I followed the GROMACS  "Doing Restarts" section, however it does not
> > work as expected; the trajecory and energy files are reinitialized and I
> > lost most of the MD informations.
> > Only log files were updated as expected.
>
> Is this with the latest GROMACS version? If not, please try that.
>
> Mark